[Biopython-dev] Deprecating Bio.PDB.PSEA

[Peter Cock]

Thanks Patrick,

Sourav - If there are no objections, then next week I suggest
you make a pull request to do the deprecation.

Regards,

Peter

On Thu, Jul 27, 2017 at 3:30 PM, Patrick Kunzmann
<padix.kleber at gmail.com> wrote:
> There are also no objections from my side. If the algorithm is well
> documented and implementation using numpy arrays is feasible, I might
> integrate it in my onging develoment of a new structure subpackage.
>
> Best regards,
>
> Patrick
>
>
>
> On 27.07.2017 10:50, Peter Cock wrote:
>>
>> This came up in discussion on this pull request:
>>
>> https://github.com/biopython/biopython/pull/1336
>>
>> Quoting the tool's README file,
>>
>> "P-SEA is small tool for secondary structure assignment
>> from Ca cartesian coordinates of proteins. It reads
>> PDB-formatted file and return a file containing : the
>> sequence read in one-letter code and the secondary
>> structure assigned (a=helix, b=strand, c=coil)."
>>
>> It does compile fine on macOS Sierra, and the readme
>> talks about other Unix platforms (HP-UX and IRIX),
>> but it does not compile as is on Linux.
>>
>> In either case you get warnings about using the "gets"
>> function which is not secure.
>>
>> I favour deprecating Bio.PDB.PSEA
>>
>> Peter
>>
>>
>> On Wed, Jul 26, 2017 at 7:13 PM, Sourav Singh <ssouravsingh12 at gmail.com>
>> wrote:
>>>
>>> Hello,
>>>
>>> As referenced in the subject, I would like to discuss about deprecating
>>> Bio.PDB.PSEA
>>>
>>> As referenced in the link here-
>>> ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/P-SEA.tar.gz
>>>
>>> The last update to the P-SEA package was done in September 1996, which
>>> makes
>>> it really old. I would like to know if the dev community is fine with
>>> deprecating the module for future releases of Biopython.
>>>
>>> Regards,
>>>
>>> Sourav
>>>
>>> Sent from my Phone.Excuse any mistakes and brevity.
>>>
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>>
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